Breeding Science最新文献

Stem length is a crucial agronomic trait in rice breeding. The short stature of rice dwarf mutants is caused by shortening of internodes, resulting in five distinct internode elongation patterns: dn, dm, d6, nl and sh. Several genetic studies have been conducted; however, the genetic mechanisms underlying these internode elongation patterns remain unclear. In this study, we examined two Daikoku dwarf (d1) mutants, T65(d1-1) and Kin(d1-7), which display contrasting internode elongation phenotypes. Anatomical observation revealed that T65(d1-1) exhibits a dm-type internode elongation pattern due to the lack of the second internode counted from the top, while Kin(d1-7) shows a dn-type pattern with a relatively elongated second internode. To identify the genetic factors influencing these phenotypes, we conducted a quantitative trait locus (QTL) analysis using two F₂ populations derived from reciprocal crosses between them. The QTL analysis showed that the second internode length is regulated by three QTLs on chromosomes 4, 5, and 6. Epistatic effects were observed through the analysis of F₃ progenies, indicating that the combination of Kin(d1-7) alleles at these QTLs is associated with an increased second internode length. Furthermore, specific combinations of alleles result in varying degrees of elongation in the second internode, significantly impacting the internode elongation pattern. These findings contribute to a deeper understanding of the genetic factors influencing the internode elongation patterns in rice.

The OsNRAMP5-deficient rice (Oryza sativa L.) mutant (osnramp5-2), with a low grain cadmium (Cd) content, was registered as 'Koshihikari Kan No. 1' in Japan. Its agronomic traits are almost identical to those of 'Koshihikari' except for its low Cd content and its susceptibility to brown spot (BS) caused by Bipolaris oryzae. To restore BS resistance, we introduced the BS resistance quantitative trait locus (QTL) bsr1 into it. The resulting isogenic line (IL) had higher resistance to BS than Koshihikari Kan No. 1 while retaining low grain Cd, with no significant difference from Koshihikari in grain yield or quality. This IL, which we named 'Kanto IL 31', can be used for breeding varieties with low Cd content and BS resistance.

The cultivated peanut, Arachis hypogaea L., is an important source of edible oil and highly digestible protein. Wild incompatible Arachis species outside section Arachis are ideal gene reservoirs for genetic improvement of the peanut crop. Among these, A. glabrata Benth. stands out for its noted resistance to various stresses. Traditional in vitro embryo rescue techniques have been fraught with challenges, including time consumption, resource intensiveness, late intervention timing, and limited effectiveness. In this study, we employed three hormone formulations in an innovative in situ embryo rescue approach to facilitate the production of intersectional Arachis hybrids. Through this method, hybrid seeds resulting from the crossing of two incompatible species, namely A. glabrata and A. paraguariensis, with four high-oleic peanut varieties were successfully obtained. Molecular marker analysis and observation of plant characteristics confirmed the hybrid nature of these seeds. This breakthrough represents a significant advancement in expediting the utilization of incompatible wild Arachis species in peanut breeding programs. Moreover, the in situ embryo rescue technique showcased in this study holds promise for application in other plant species characterized by postzygotic cross-incompatibility.

Asian rice (Oryza sativa L.) was domesticated from wild rice (O. rufipogon Griff.). During rice domestication, the wild characteristic of seed-shattering behaviour was suppressed, enabling an efficient harvest with increased yield. Rice, a stable food for humans, is one of the most important crops consumed by billions of people, especially in Asian countries. With advances in molecular genetic studies, genes or loci involved in reduced seed shattering via the inhibition of abscission layer formation have been identified. The mutations alone showed no inhibitory effect on abscission layer formation in the wild rice O. rufipogon, but their combination enabled a stepwise change in the degree of seed shattering, which may be associated with advances in harvesting tools. In the early stages of rice domestication, the closed panicle formation and slight inhibition of the abscission layer resulted in complementary effects that increased harvesting efficiency. Furthermore, common and distinct loci were found to contribute to reduced seed shattering in groups of rice cultivars, indicating that mutations at seed-shattering loci are important information for tracing the process of rice domestication.

The vascular bundle system in the panicle neck of rice (Oryza sativa L.) connects the culm to the panicle and transports assimilates. The number of vascular bundles in the panicle neck (VBN) is correlated with the diameter of the panicle neck (DPN), but there are few reported QTLs for DPN. We conducted quantitative trait locus (QTL) analysis using recombinant inbred lines (RILs) derived from a cross between 'Asominori' and 'IR24' and detected three QTLs-qDPN5, qDPN6, and qDPN11-on chromosomes 5, 6, and 11. The qDPN5, qDPN6, and qDPN11 were in the same position as the QTLs for VBN reported in previous studies. Within the RILs, there was a significant positive correlation between DPN and VBN. In segregating populations, each QTL had a distinct effect on both values. Analysis of chromosome segment substitution lines showed that qDPN5 and qDPN11 affected DPN and qDPN6 affected VBN. Through substitution mapping, we narrowed down the region of qDPN5 and qVBN5.2 to 960 kbp between KNJ8 Indel385 and RM18926, and the region of qVBN6 to 750 kbp between C5 Indel5756 and KNJ8 Indel493. Due to the weak effect of qDPN6 in the 'IR24' genetic background, the location of qDPN6 could not be determined.

The introgression of heterologous genomes through interspecific hybridization offers a great opportunity to expand the gene pool of crops, thereby broadening the traits that can be targeted for improvement. The introgression of C genomic regions carrying desirable traits from Brassica napus (AACC) into the diploid B. rapa (AA) via homoeologous recombination (HR) has been commonly used. However, the precise identification of HR sites remains a significant challenge, limiting the practical application of genome introgression via HR in breeding programs. Here, we developed an indicator named 'Dosage-score' from the coverage depth of next-generation sequencing reads. Then, Dosage-score analysis applied to both in BC₁F₁ individuals obtained by backcrossing B. rapa to F₁ progeny (B. rapa × B. napus) and in the parental lines, and successfully identified the precise HR sites resulting from F₁ meiosis as well as those that were native in the parental B. napus genome. Additionally, we introgressed the C6 segment from HR identified by Dosage-score analysis into B. rapa genome background, revealing gene expression on the added segment without noticeable phenotypic change. The identification of HR by Dosage-score analysis will contribute to the expansion of the gene pool for breeding by introgression of heterologous genomes in Brassica crops.

To explore the molecular mechanism behind maize grain quality and use of different gene stacking to improve the nutritional quality of grain, marker-assisted selection (MAS) was used to select three recessive mutant lines containing o2o16wx, along with the double-recessive mutant lines containing o2o16, o2wx, and o16wx. The resulting seeds were taken for transcriptome sequencing analysis 18 days after pollination (DAP). Results: Compared with the recurrent parent genes, in the lysine synthesis pathway, the gene pyramiding lines (o2o16wx, o2wx, and o16wx) revealed that the gene encoding aspartate kinase (AK) was up-regulated and promoted lysine synthesis. In the lysine degradation pathway, 'QCL8010_1' (o2o16wx) revealed that the gene encoding saccharopine dehydrogenase (LKR/SDH) was down-regulated. In addition, the gene pyramiding lines (o2o16wx, o2o16, and o16wx) indicated that the gene encoding 2-oxoglutarate dehydrogenase E1 component (OGDH) was down-regulated, inhibiting the degradation of lysine. In the tryptophan synthesis pathway, the genes encoding anthranilate synthase (AS), anthranilate synthase (APT), and tryptophan synthase (TS) were up-regulated (in o2o16wx, o2o16, o2wx, and o16wx), and promote tryptophan synthesis. In the tryptophan degradation pathway, it was revealed that the genes encoding indole-3-producing oxidase (IAAO) and indole-3-pyruvate monooxygenase (YUCCA) were down-regulated. These results provide a reference for revealing the mechanism of the o2, o16, and wx with different gene pyramiding to improve grain quality in maize.

Tomatoes have the highest agricultural production among vegetables in Japan and worldwide. Japanese large-sized fresh-market tomatoes have a unique breeding history that differs from that of other countries, represented by pink-colored and juicy fruits with a good taste and flavor. We performed whole-genome resequencing of 150 Japanese large-sized fresh-market tomato cultivars released from the 1940s to the 2000s to unveil how breeding selection has changed the genome of Japanese tomato cultivars and provide a genomic basis for future Japanese tomato breeding. The genomic population structure of the cultivars was highly correlated with the year of release. Comparison between the agronomic performance and release year of the cultivars reflected trends in recent breeding selection: an increase in fruit sugar content and a decrease in yield performance. Multiple selection signatures were detected on all the tomato chromosomes. One of the selection signatures was related to the introgression of a resistance gene (Tm-2) from a wild relative. Interestingly, some of the putative QTLs detected by genome-wide association studies did not co-localize with the selection signatures, indicating that the genetic diversity of Japanese tomato cultivars still has the potential for genetic improvement of agronomic performance.

Turnip mosaic virus (TuMV) poses a major threat to Brassica crops like Chinese cabbage, causing significant economic losses. A viable and effective strategy to manage such diseases is by improvement of genetic-based viral resistance. To achieve this, it is important to have detailed and wide-ranging genetic resources, necessitating genetic exploration. To identify useful TuMV resistant genetic resources, we screened geographically and genetically diverse resources including over 90 accessions from the Tohoku Univ. Brassica Seed Bank against eleven TuMV isolates phylogenetically classified into five clusters. Two USA accessions exhibited no or only slight symptoms with no virus protein detected in virus-inoculated and non-inoculated upper leaves, suggesting an extreme resistance to all tested TuMV isolates. Through sequencing and dCAPS analysis of eukaryotic translation initiation factor (eIF4E/eIFiso4E) in the 95 B. rapa accessions, several amino acid substitutions were observed on the dorsal surface and cap-binding sites of eIF4E/eIFiso4E proteins, with three of them significantly associated with resistance/susceptibility responses. When exploring co-infection using TuMV and cucumber mosaic virus (CMV), the TuMV susceptible accession died, but TuMV resistance was retained in the TuMV resistant accession. It suggested that the broad-spectrum resistance in the two USA accessions is a highly valuable resources for Brassica breeding.

Green rice leafhopper (GRH, Nephotettix cincticeps Uhler) is a serious insect pest of rice in the temperate regions of Asia. Myanmar has a high genetic diversity and is located at the center of the origin of rice. To understand the genetic architecture of GRH resistance in Myanmar indica rice landraces, a genome-wide association study (GWAS) was performed using a diversity panel collected from diverse geographical regions. Phenotypic variation in GRH resistance was associated with three genomic regions, MTA4, MTA5, and MTA11, located on chromosomes 4, 5, and 11, respectively. MTA4 and MTA5 were adjacent to the known resistance genes GRH6 and GRH1. Analysis of haplotypes and linkage disequilibrium blocks revealed that the haplotypes HapGRH6A, HapGRH1A, and HapMTA11A mainly explained GRH resistance. Map-based cloning revealed that GRH6 was highly induced by GRH infestation and conferred resistance by inhibiting the sucking of phloem sap. The distribution of resistance haplotypes revealed that accessions harboring major resistance haplotypes (HapGRH6A and HapGRH1A) were mainly distributed in Southern Myanmar, and HapMTA11A was mainly responsible for GRH resistance in mountainous areas of Myanmar. Our findings could facilitate the elucidation of the molecular mechanism of GRH resistance and provide essential haplotype-based genetic information for the development of GRH-resistant rice cultivars.